Move IIS SMTP Dir

First:

create your new folder locations (this can be done by copying the
current inetpub folder to a different drive/partition) or manually creating
the necessary folders

Second:

to move the websites use IIS Manager (right-click on each website,
and update the root of each website). You can do this programmatically by
using adsutil.vbs

Third:

do the same for the FTP sites

Fourth:

to move the SMTP service's folders, use the following script:
(watch for wrapping!), they are

"cscript.exe [directory]/[file.vbs] set smtpsvc/1/[command] [dir destination]

cscript.exe c:\inetpub\adminscripts\adsutil.vbs set smtpsvc/1/dropdirectory E:\Repository\Inetpub\mailroot\drop
cscript.exe c:\inetpub\adminscripts\adsutil.vbs set smtpsvc/1/badmaildirectory E:\Repository\Inetpub\mailroot\badmail
cscript.exe c:\inetpub\adminscripts\adsutil.vbs set smtpsvc/1/pickupdirectory E:\Repository\Inetpub\mailroot\pickup
cscript.exe c:\inetpub\adminscripts\adsutil.vbs set smtpsvc/1/queuedirectory E:\Repository\Inetpub\mailroot\queue

Change x:\mailroot to be the place you want the other folders to go into.